Question: Upload Data To Sra Without Taxonomy Id
1
gravatar for GAO Yang
7.5 years ago by
GAO Yang250
GAO Yang250 wrote:

Hi there~

I want to upload some transcriptome raw reads that I sequenced, to the SRA database.

But one of the samples (sample J ) was a artificial hybrid progeny of two other species, and even not officially defined as a new specie yet. So , sample J won't have the Taxon ID which is necessary for the submission.

What should i do? Should I use the Taxon ID of one of the parental species (father/mother)? Or should I apply for a new taxon ID even it has not been accepted as a new specie?

Any suggestion, discussion or information will be greatly appreciated!

Thank you!

sra • 1.5k views
ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by GAO Yang250
2

I'd suggest contacting SRA directly. This is an important question and impacts the utility of the SRA database.

ADD REPLYlink written 7.5 years ago by Sean Davis26k

To expand on Sean's adice - if you do get the information from SRA please consider following up here and adding it as an answer.

ADD REPLYlink written 7.5 years ago by Istvan Albert ♦♦ 83k
0
gravatar for GAO Yang
7.5 years ago by
GAO Yang250
GAO Yang250 wrote:

Yeah, I wrote 2 letters, one for NCBI, the other one directly to SRA. And both were replied soon :) The letter from NCBI services suggested me to apply for new taxon ID, and I should contact SRA for sure.

The letter from SRA said I could just used the taxon ID of either of parental species, and then explained in the sample description. Simple!

Now I am going to upload the data files, as soon as got the password for the SRA ftp server.

ADD COMMENTlink written 7.5 years ago by GAO Yang250

interesting, thanks for following up

ADD REPLYlink written 7.5 years ago by Istvan Albert ♦♦ 83k

This approach seems less than optimal. SRA metadata should be computable, so suggesting to include what is essentially known contamination in a "note" seems counter to that. This is a problem for SRA, but I just wanted to point out that this an obvious problem with the suggested solution.

ADD REPLYlink written 7.5 years ago by Sean Davis26k
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